I wrote my own response in Equestria Daily's combox, and I reproduce it here:

It took me a while to put together all my thoughts on
this matter, and the discussion on this site has likely moved on since this was
posted, but here goes anyway:

A short while ago, I was in India. While I was there, I frequently saw men
holding hands with each other or putting their arms over each other’s
shoulders. I volunteered in an
orphanage, and the older boys would often walk up to me or sit beside me and
interlace their fingers with mine. Every
guidebook I read on that trip mentioned this type of behavior and explained
that this was a sign of friendship, not homosexuality. That the writers of these guidebooks felt the
need to put in such a notice says, I think, more about our culture than it says
about India.

Analogously, ponies in the My Little Pony franchise
have been licking and cuddling each other since the early 1980s, but only
recently has anyone taken this to be an indication that the ponies are
lesbians. Again, I think this says less
about the franchise than it says about our culture and how it has changed in
the last three decades. For quite some
time, we have been in the business of sexualizing most everything, but in
recent days, that has apparently grown uninteresting, so now we have begun
homosexualizing everything, including, apparently, innocent children’s cartoon
shows.

The debate over homosexuality is often presented as an
argument being had by Christians against everybody else, but that’s not
actually the case. For one thing, the
current laissez-faire attitude toward sexuality is unique to the postmodern and
post-Christian West. It has existed for
only a short while in a limited (though large) geographic location, and it is
probably not long to endure. Those who
advocate it may think they are being cosmopolitan, but they are in fact being
quite parochial and myopic.

For another thing, the arguments involved run deep. The debate over homosexuality is in the end,
at least from what I’ve seen it, not so much an argument between Christians and
non-Christians as it is an argument between hylemorphists and materialists,
between Aristotelians and Nominalists, between deontologists and
consequentialists. But almost no one
studies philosophy anymore, so most who address this topic muddle through
without ever stating or evaluating the fundamental axioms on which their
positions rest. Modern thought is
characterized, probably more than anything else, by confusion, by an inability
to define terms, by an inability to make distinctions, by an inability to use logic. Many people who defend homosexual acts as
normal or advocate for homosexual marriage seem to be honestly incapable, for
example, of making even the simple and obvious distinction between copulation
and mutual masturbation.

It appears to me, too, that this confusion of modern
thought is on display in the Brony community, particularly in the popular
slogan, “Love and tolerate.” To love
means to will the good of someone for his own sake. To tolerate, on the other hand, means to allow
or put up with another’s behavior no matter what you think of it. The two are mutually exclusive: you cannot possibly tolerate the
self-destructive behavior of someone you love.
The Brony slogan is a meaningless paradox.

Very briefly and inadequately, I will lay out the
position I hold on the subject of homosexuality.

It begins with teleology, the study of final causes or
ends. Though it is popular to deny their
existence, final causes exist, and this is evident in that it is impossible to
avoid them. Take an eye as an easy example: you could describe it down to the last atom,
but until you say that an eye is for seeing--that’s its purpose, or end--you
have not fully described it. Similarly,
the purpose of the genitals is generation (hence the name), and the purpose of
the sexual appetite is procreation, that is, reproduction. If an appetite is directed toward something
out of accordance with its purpose, it can be described as “disordered.” That is merely descriptive; it is not an
ethical judgment. If I, say, hunger to
eat rocks instead of eat food, I have a disordered appetite.

All of that is relatively simple. Note, please, that the existence of final
causes does not imply the existence of God, though many today are inclined to
leap to the conclusion that it does, which is why arguments beginning with
teleology are often dismissed as religious.
There are arguments from final causes to the existence of God, but they
are long and complicated and questionable at some points. The one does imply the other.

Ethically, to live a rational life of virtue, it is
necessary to govern the appetites and passions with the reason. Appetites are not reasonable in
themselves. I may desire to eat two
entire cakes all by myself, Celestia-style, but I must judge with my reason that
doing so would be bad for me. My
appetite is immoderate, and so I must resist it. If I do not, the results will be a decreased
ability to resist it in the future, a likely growth in the immoderation of the
appetite, and, in the long run, poor health.

The way to judge the appetites is to determine if they
are within the bounds set by the purposes for which they exist. The primary purpose of the appetite for food
is to nourish the body. Eating is also
pleasurable, of course, but if I eat merely for my own pleasure without concern
for my health, I will reap the consequences.
I assume this is obvious.

The primary purpose of the appetite for sex is
reproduction. This should also be
obvious, though many today are in the business of denying it. If the appetite is directing me to copulate
with something with which it is actually impossible to copulate, such as an
inanimate object or a member of the same sex, the appetite is disordered. My ethical obligation, as in the case of an
immoderate or disordered appetite for food, is to resist its impulses.

From this, it can be seen first of all that a person
is not morally culpable for having a disordered appetite, so whenever someone
asks me if I think “homosexuality” is immoral, I have to heavily qualify the
question before I can answer it. It can
also be seen that homosexual acts are not morally licit.

Now I’ll bring all of this around to the discussion of
fan fiction and of the essay linked in this post.

First, to deal with some of the claims of the essayist
and the claims of some Bronies that the show actually contains a homosexual
subtext, I refer back to the paragraphs with which I opened this. We have taken on the habit of interpreting
any amount of affection between members of the same sex as signs of
homosexuality, and I believe this is to our detriment; it severely hinders
members of the same sex from having close or affectionate platonic
relationships. The show, far from
presenting a homosexual subtext, actually serves as a counterpoint to
this. The show is not about lesbians; it’s
about friends. To claim that Glinda must
have been Rainbow Dash’s old girlfriend, or that something subtle is going on
between Rainbow Dash and Applejack in “Fall Weather Friends,” or that Rainbow
Dash and Fluttershy are definitely lesbians because Rainbow gives Fluttershy a
hug in “Hurricane Fluttershy,” is to miss the point: the show is about friendship, as it says right
in the title. The characters are
affectionate because they’re friends, and if you don’t understand that, I’m
afraid you just don’t “get” the show.

And as for Lyra and Bon-Bon, the claim that they’re
lesbians in canon sounds almost like a bad tavern joke: “Hey, I saw two ponies standing next to each
other in the background, and you know what they say about two ponies who stand
next to each other in the background.”

During the controversy over Rainbow Dash’s ambiguous
peck on Fluttershy’s nose in the season finale, I found a comment in a
discussion thread that I think sums things up very nicely. I’d probably never be able to find it again,
so I’ll paraphrase: “Listen, guys,
sometimes girls kiss each other, particularly during stressful or emotional
moments, and it doesn’t mean they’re lesbians.
Now go back to your basement.”

To wrap this up, I am not opposed to any and all
depiction of homosexuality in literature, fan-created or otherwise. Disordered desires are things that real
people struggle with, and it would be strange to ban their depiction from
literature. However, if someone writes a
homosexual romance and writes it as if it’s really no different from heterosexual
romance, or as if anyone who points out that it’s different from heterosexual
romance should feel bad about himself, I probably won’t bother to read it because the author is revealing that he doesn’t
understand his subject matter. Many of
the components of romance may be present in the story, and it may have all the
emotions of romance, but the fundamental reason romance exists in the first
place is absent. The author is revealing
that he doesn’t understand love, doesn’t understand courtship, doesn’t
understand marriage, and doesn’t even understand sex.

An author I respect said something on this subject I’d
like to repeat; he was writing under a handle at the time, which might mean he
didn’t want to be named, so I’ll summarize his statement without giving
credit: To love means to will the good
of another person, but in recent times, we’ve decided you can’t really love
anything without trying to have sex with it.
In the modern mind, love has been replaced with self-pleasure.

A friend and fellow Brony whom I converted to Bronyism to the endangerment of both our souls sends me a link to a relevant article on the subject, "A Requiem for Male Friendship?" over at Musings of a Pertinacious Papist. The pertinacious one fleshes out and argues cogently for a belief I've held for years: the prevalence of homosexuality in our culture kills the possibility of strong same-sex friendships. The Brony obsession with lesbianism is an extreme and absurd example of this: even cartoon ponies can no longer have strong same-sex friendships; there are fans of the show who honestly believe the physically sexless anthropomorphized horse-like cartoon characters must be homosexuals because they've sometimes been seen hugging each other, or because one of them is rainbow-colored (Like, dude, do you even freaking remember what it is you're watching??? There's freaking rainbows freaking everywhere in this freaking franchise . . . oops, sorry; little fanboy outburst there).